The “Omicron” variant has prevailed at 87% in Attica, while at the same time the respective genetic indicators of the Delta strain have significantly decreased, according to the analysis of EKPA in the wastewater, during the period 27-12-2021 to 1-1-2022.

At the National and Kapodistrian University of Athens (EKPA), through collaboration
Research Units of the Departments of Biology, Medicine and Chemistry, in the context of research
with Scientific Officer Professor Andreas Skorilas and his interdisciplinary team
EKPA consisting of Nikolaos Thomaidis, Margariti Avgeri, Athena Markou, Evi
Lianidou, Dimitrios Gourgiotis, Theodora Psaltopoulou, Panagiotis Adamopoulos, Mario
Diamantopoulos, Lambros Dimitrakopoulos, Katerina Galani, Mario Kostaki, Katerina
Kontou, Vassilis Kape, Nikolaos Voulgaris and Thanos Dimopoulos (Rector of EKPA), has
develop a new molecular methodology for sensitive detection and quantification
of mutant strains / variants of SARS-CoV-2 in wastewater samples using a series of molecular methods and Next Generation sequence
Sequence / NGS).

This hypersensitive methodology is especially important because it shows
the presence and percentage analysis of the mutant strains as a whole
population of a city. In addition, it detects in time, even from 50ml of sewage or
any environmental sample, new mutations and strains / variants that
as soon as they began to enter the population. This way it becomes bigger
genomic surveillance of new strains / variants of SARS-CoV-2, as well as other viruses or bacteria, providing the necessary information for epidemiological surveillance as well as the redesign of new vaccines and
pharmaceutical protocols.

The relevant article was published in the prestigious international scientific journal “International Journal of Molecular Sciences”, while an application for the grant of National and International Patents has been submitted by EKPA.

The methodology meets the conditions of its relevant recommendation from 15-3-2021
Common Approach in creating a systematic approach
SARS-CoV-2 and its variants in wastewater. In addition, it detects
timely new strains / variants that begin to enter the community.
With the application of the new methodology, the analysis of mutants has been completed
of SARS-CoV-2 strains in wastewater samples of the Attica Regional Unit, which
were collected on a daily basis during the period 27-12 / 2021 to 1-1-2022 by the Wastewater Treatment Center of Psyttalia (KELD).

The specific samples were tested for specific mutations – genetic markers (genetic markers) of the entire S gene (Spike) (> 100 genetic markers) for the variants of special interest (Variants of Concern – VOC) and the variants under investigation (Variants of Interest – VOI).

The results of the analysis showed the prevalence, at a rate of 87% with
significant diversity, of the Omicron variant (B.1.1.529 lineage) and the simultaneous
significant reduction in the genetic marker correspondences of the Delta strain (B.1.617.2
origin).

More specifically, the presence of specific mutations (genetic markers) was detected
of the S gene (Spike) of the Omicron variant (B.1.1.529 lineage):

– in the section “receptor-binding domain / RBD” at a rate of 87% (genetic markers: G339D, S371L, S373P, S375F, K417N, N440K, G446S)

– in the section “receptor-binding motif / RBM” at a rate of 29% (genetic markers: S477N, E484AQ493R, G496S, Q498R, N501Y, Y505H)

– excluding RBD / RBM segments at 45% (genetic markers: T547K, H655Y, N679K,
P681H, N764K, D796Y, N856K, Q954H, N969K, L981F) 2

At the same time, the presence of two of its executives was confirmed for the first time
Omicron variants, which carry (co-mapped) additional mutations, namely:

– the mutation R346K (B.1.1.529 + R346K), at a rate of 27%, which has been reported in
Mu variant (B1.621)

– the A701V mutation (B.1.1.529 + A701V), at a rate of 5%, reported in
Beta variant (B1.351)

Based on the above results, the predominance of the variant is ascertained
Homicron in Attica (at a rate of 87% from and 40% 2 weeks ago) as well as
corresponding reduction of the Delta variant.

At the same time, the sequence of the virus genome is important
variability of the percentage of specific mutations of the S gene, which
encodes the Spike protein, emphasizing its different significance and weight
in the behavior of the virus, as well as in its reliable and specific identification.

The analysis of the next generation sequence data with the above
method further shows that in addition to variability there are several combinations of different mutations in the virus, which may prevail each time with different clinical behavior, which requires vigilance and faithful implementation of the measures.

Elena Bregianni